Abstract: Microorganisms are ubiquitous in nature, and have special function in degraded plant cell wall. In the animal gastrointestinal tract, the microorganisms is closely related with the growth and metabolism of the host, because of the degraded function contributed to transform plant to nutrition for the animal. Meanwhile, with the techniques and analysis methods improved, modern metagenomics, based on the high-throughout sequencing, was enable us to study microbia in complex environment more convenient. Using modern metagenomics techniques on the animal gastrointestinal microbial could conduce to a greater extent mining functional gene of microbial gene pool, which was not only played an important guiding role in the growth regulation, disease prevention and other basic science of animal, but also in the industrial production, food security and other fields. This review showed the research of metagenomic technology in animal gastrointestinal microbial classification, application etc., in order to provide scientific reference for animal production, microbial fermentation and other related field.

Key words: rumen microbe, intestinal microbia, metagenomics, 16S rRNA

摘要： 微生物在自然界普遍存在,且具有降解植物细胞壁的特殊功能。动物胃肠道寄生的微生物与宿主生长发育和机体代谢密切相关，可以帮助动物将植物源性物质转化为机体所需要的营养物质。基于高通量测序的宏基因组学技术和分析方法的改进，使人们对复杂环境中微生物的研究更加方便、透彻。而宏基因组学技术应用于动物胃肠道微生物的研究，则有助于挖掘胃肠道微生物基因库并筛选其中的功能基因。这不仅对动物生长发育调控、疾病预防等基础研究具有重要意义，而且在工业生产及食品安全等领域也发挥着重要作用。就基于高通量测序技术的宏基因组技术在动物胃肠道微生物分类、功能应用等方面的研究进行了梳理和综述，旨在为动物科学生产及微生物发酵等相关领域的研究工作提供科学指导。

关键词: 瘤胃微生物, 肠道微生物, 宏基因组学, 16S rRNA